Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1988 Aug 11;16(15):7419–7436. doi: 10.1093/nar/16.15.7419

Conserved elements in the transcription initiation regions preceding highly expressed structural genes of methanogenic archaebacteria.

R Allmansberger 1, S Knaub 1, A Klein 1
PMCID: PMC338418  PMID: 3412892

Abstract

The sequences of the intergenic regions of the strongly expressed genes encoding methyl CoM reductase in three different methanogenic archaebacteria were determined and the 5'-ends of the transcripts were mapped. After alignment, consensus sequences were found which are located both upstream and downstream of the transcription starts. They correspond, in part, to those previously characterized as putative elements of archaebacterial promoter sequences. In addition, bending of the DNA in front of the transcription start sites was shown in two cases and a characteristic common DNA structure immediately downstream of the 5'-end of the transcript was discovered. This structure was also found in the corresponding regions of previously described genes in methanogens. Our results suggest that both sequence and structural information may have roles in the initiation of transcription of protein encoding genes of these archaebacteria.

Full text

PDF
7419

Images in this article

7424Image
on p.7424
7425Image
on p.7425
7426Image
on p.7426
7427Image
on p.7427
7428Image
on p.7428
7429Image
on p.7429

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bokranz M., Bäumner G., Allmansberger R., Ankel-Fuchs D., Klein A. Cloning and characterization of the methyl coenzyme M reductase genes from Methanobacterium thermoautotrophicum. J Bacteriol. 1988 Feb;170(2):568–577. doi: 10.1128/jb.170.2.568-577.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bokranz M., Klein A. Nucleotide sequence of the methyl coenzyme M reductase gene cluster from Methanosarcina barkeri. Nucleic Acids Res. 1987 May 26;15(10):4350–4351. doi: 10.1093/nar/15.10.4350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bollschweiler C., Kühn R., Klein A. Non-repetitive AT-rich sequences are found in intergenic regions of Methanococcus voltae DNA. EMBO J. 1985 Mar;4(3):805–809. doi: 10.1002/j.1460-2075.1985.tb03701.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brown J. W., Thomm M., Beckler G. S., Frey G., Stetter K. O., Reeve J. N. An archaebacterial RNA polymerase binding site and transcription initiation of the hisA gene in Methanococcus vannielii. Nucleic Acids Res. 1988 Jan 11;16(1):135–150. doi: 10.1093/nar/16.1.135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Burkhoff A. M., Tullius T. D. The unusual conformation adopted by the adenine tracts in kinetoplast DNA. Cell. 1987 Mar 27;48(6):935–943. doi: 10.1016/0092-8674(87)90702-1. [DOI] [PubMed] [Google Scholar]
  6. Calladine C. R. Mechanics of sequence-dependent stacking of bases in B-DNA. J Mol Biol. 1982 Oct 25;161(2):343–352. doi: 10.1016/0022-2836(82)90157-7. [DOI] [PubMed] [Google Scholar]
  7. Cue D., Beckler G. S., Reeve J. N., Konisky J. Structure and sequence divergence of two archaebacterial genes. Proc Natl Acad Sci U S A. 1985 Jun;82(12):4207–4211. doi: 10.1073/pnas.82.12.4207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Dickerson R. E. Base sequence and helix structure variation in B and A DNA. J Mol Biol. 1983 May 25;166(3):419–441. doi: 10.1016/s0022-2836(83)80093-x. [DOI] [PubMed] [Google Scholar]
  9. Ellefson W. L., Wolfe R. S. Component C of the methylreductase system of Methanobacterium. J Biol Chem. 1981 May 10;256(9):4259–4262. [PubMed] [Google Scholar]
  10. Klein A., Schnorr M. Genome complexity of methanogenic bacteria. J Bacteriol. 1984 May;158(2):628–631. doi: 10.1128/jb.158.2.628-631.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
  12. Lu P., Cheung S., Arndt K. Possible molecular detent in the DNA structure at regulatory sequences. J Biomol Struct Dyn. 1983 Oct;1(2):509–521. doi: 10.1080/07391102.1983.10507458. [DOI] [PubMed] [Google Scholar]
  13. McClure W. R. Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem. 1985;54:171–204. doi: 10.1146/annurev.bi.54.070185.001131. [DOI] [PubMed] [Google Scholar]
  14. Müller B., Allmansberger R., Klein A. Termination of a transcription unit comprising highly expressed genes in the archaebacterium Methanococcus voltae. Nucleic Acids Res. 1985 Sep 25;13(18):6439–6445. doi: 10.1093/nar/13.18.6439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Plaskon R. R., Wartell R. M. Sequence distributions associated with DNA curvature are found upstream of strong E. coli promoters. Nucleic Acids Res. 1987 Jan 26;15(2):785–796. doi: 10.1093/nar/15.2.785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Reiter W. D., Palm P., Zillig W. Analysis of transcription in the archaebacterium Sulfolobus indicates that archaebacterial promoters are homologous to eukaryotic pol II promoters. Nucleic Acids Res. 1988 Jan 11;16(1):1–19. doi: 10.1093/nar/16.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Reiter W. D., Palm P., Zillig W. Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation. Nucleic Acids Res. 1988 Mar 25;16(6):2445–2459. doi: 10.1093/nar/16.6.2445. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Schnabel R., Thomm M., Gerardy-Schahn R., Zillig W., Stetter K. O., Huet J. Structural homology between different archaebacterial DNA-dependent RNA polymerases analyzed by immunological comparison of their components. EMBO J. 1983;2(5):751–755. doi: 10.1002/j.1460-2075.1983.tb01495.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Stenzel T. T., Patel P., Bastia D. The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101. Cell. 1987 Jun 5;49(5):709–717. doi: 10.1016/0092-8674(87)90547-2. [DOI] [PubMed] [Google Scholar]
  20. Struhl K. Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci U S A. 1985 Dec;82(24):8419–8423. doi: 10.1073/pnas.82.24.8419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Thomm M., Wich G. An archaebacterial promoter element for stable RNA genes with homology to the TATA box of higher eukaryotes. Nucleic Acids Res. 1988 Jan 11;16(1):151–163. doi: 10.1093/nar/16.1.151. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  23. Wich G., Hummel H., Jarsch M., Bär U., Böck A. Transcription signals for stable RNA genes in Methanococcus. Nucleic Acids Res. 1986 Mar 25;14(6):2459–2479. doi: 10.1093/nar/14.6.2459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Woese C. R., Fox G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088–5090. doi: 10.1073/pnas.74.11.5088. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES